The pH within the lysosome is about pH 5, substantially less than that of the cytosol (~pH 7.2). All the enzymes in the lysosome work best at an acid pH. This reduces the risk of their digesting their own cell if they should escape from the lysosome.

At one time, it was thought that lysosomes were responsible for killing cells scheduled to be removed from a tissue; for example, the resorption of its tail as the tadpole metamorphoses into a frog. This is incorrect. These examples of programmed cell death (PCD) or apoptosis take place by an entirely different mechanism. Link to a discussion of apoptosis.

Materials within the cell scheduled for digestion are first deposited within lysosomes. These may be:

other organelles, such as mitochondria, that have ceased functioning properly and have been engulfed in autophagosomes

food molecules or, in some cases, food particles taken into the cell by endocytosis

Lysosomal storage diseases are caused by the accumulation of macromolecules (proteins, polysaccharides, lipids) in the lysosomes because of a genetic failure to manufacture an enzyme needed for their breakdown. Neurons of the central nervous system are particularly susceptible to damage.

Most of these diseases are caused by the inheritance of two defective alleles of the gene encoding one of the hydrolytic enzymes.

Examples:

Tay-Sachs disease and Gaucher's disease — both caused by a failure to produce an enzyme needed to break down sphingolipids (fatty acid derivatives found in all cell membranes).

Mucopolysaccharidosis I (MPS-I). Caused by a failure to synthesize an enzyme (α-L-iduronidase) needed to break down proteoglycans like heparan sulfate. In April 2003, the U.S. Food and Drug Administration approved a synthetic version of the enzyme, laronidase (Aldurazyme®), as a possible treatment. This enzyme (containing 628 amino acids) is manufactured by recombinant DNA technology.

However, one lysosomal storage disease, I-cell disease ("inclusion-cell disease"), is caused by a failure to "tag" (by phosphorylation) all the hydrolytic enzymes that are supposed to be transported from the Golgi apparatus to the lysosomes. Lacking the mannose 6-phosphate (M6P) tag, they are secreted from the cell instead.

Peroxisomes are about the size of lysosomes (0.5–1.5 µm) and like them are enclosed by a single membrane. They also resemble lysosomes in being filled with enzymes.

In humans, new peroxisomes are formed by the fusion of vesicles released by the endoplasmic reticulum with vesicles released by mitochondria. Once formed, peroxisomes can then increase their number by growth and division.

The enzymes and other proteins destined for peroxisomes are synthesized in the cytosol. Each contains a peroxisomal targeting signal (PTS) that binds to a receptor molecule that takes the protein into the peroxisome and then returns for another load.

A variety of rare inherited disorders of peroxisome function occur in humans.

Most involve mutant versions of one or another of the enzymes found within peroxisomes.

Example: X-linked adrenoleukodystrophy (X-ALD). This disorder results from a failure to metabolize fatty acids properly. One result is deterioration of the myelin sheaths of neurons. The disorder occurs in young boys because the gene is X-linked. An attempt to find an effective treatment was the subject of the 1992 film Lorenzo's Oil. Since then a number of X-ALD patients have been successfully treated by gene therapy.

A few diseases result from failure to produce functional peroxisomes.

Example: Zellweger syndrome.
This disorder results from the inheritance of two mutant genes for one of the receptors (PXR1) needed to import proteins into the peroxisome.